Distinguishing between recent balancing selection and incomplete sweep using deep neural networks

Balancing selection is an important adaptive mechanism underpinning a wide range of phenotypes. Despite its relevance, the detection of recent balancing selection from genomic data is challenging as its signatures are qualitatively similar to those left by ongoing positive selection. In this study, we developed and implemented two deep neural networks and tested their performance to predict loci under recent selection, either due to balancing selection or incomplete sweep, from population genomic data. Specifically, we generated forward-in-time simulations to train and test an artificial neural network (ANN) and a convolutional neural network (CNN). ANN received as input multiple summary statistics calculated on the locus of interest, while CNN was applied directly on the matrix of haplotypes. We found that both architectures have high accuracy to identify loci under recent selection. CNN generally outperformed ANN to distinguish between signals of balancing selection and incomplete sweep and was less affected by incorrect training data. We deployed both trained networks on neutral genomic regions in European populations and demonstrated a lower false-positive rate for CNN than ANN. We finally deployed CNN within the MEFV gene region and identified several common variants predicted to be under incomplete sweep in a European population. Notably, two of these variants are functional changes and could modulate susceptibility to familial Mediterranean fever, possibly as a consequence of past adaptation to pathogens. In conclusion, deep neural networks were able to characterize signals of selection on intermediate frequency variants, an analysis currently inaccessible by commonly used strategies

From early stress to 12-month development in very preterm infants: Preliminary findings on epigenetic mechanisms and brain growth

Very preterm (VPT) infants admitted to Neonatal Intensive Care Unit (NICU) are at risk for altered brain growth and less-than-optimal socio-emotional development. Recent research suggests that early NICU-related stress contributes to socio-emotional impairments in VPT infants at 3 months through epigenetic regulation (i.e., DNA methylation) of the serotonin transporter gene (SLC6A4). In the present longitudinal study we assessed: (a) the effects of NICU-related stress and SLC6A4 methylation variations from birth to discharge on brain development at term equivalent age (TEA); (b) the association between brain volume at TEA and socio-emotional development (i.e., Personal-Social scale of Griffith Mental Development Scales, GMDS) at 12 months corrected age (CA). Twenty-four infants had complete data at 12-month-age. SLC6A4 methylation was measured at a specific CpG previously associated with NICU-related stress and socio-emotional stress. Findings confirmed that higher NICU-related stress associated with greater increase of SLC6A4 methylation at NICU discharge. Moreover, higher SLC6A4 discharge methylation was associated with reduced anterior temporal lobe (ATL) volume at TEA, which in turn was significantly associated with less-than-optimal GMDS Personal-Social scale score at 12 months CA. The reduced ATL volume at TEA mediated the pathway linking stress-related increase in SLC6A4 methylation at NICU discharge and socio-emotional development at 12 months CA. These findings suggest that early adversity-related epigenetic changes might contribute to the long-lasting programming of socio-emotional development in VPT infants through epigenetic regulation and structural modifications of the developing brain

Comfort radicalism and NEETs: a conservative praxis

Young people who are not in education, employment or training (NEET) are construed by policy makers as a pressing problem about which something should be done. Such young people's lack of employment is thought to pose difficulties for wider society in relation to social cohesion and inclusion and it is feared that they will become a 'lost generation'. This paper(1) draws upon English research, seeking to historicise the debate whilst acknowledging that these issues have a much wider purchase. The notion of NEETs rests alongside longstanding concerns of the English state and middle classes, addressing unruly male working class youth as well as the moral turpitude of working class girls. Waged labour and domesticity are seen as a means to integrate such groups into society thereby generating social cohesion. The paper places the debate within it socio-economic context and draws on theorisations of cognitive capitalism, Italian workerism, as well as emerging theories of antiwork to analyse these. It concludes by arguing that ‘radical’ approaches to NEETs that point towards inequities embedded in the social structure and call for social democratic solutions veer towards a form of comfort radicalism. Such approaches leave in place the dominance of capitalist relations as well as productivist orientations that celebrate waged labour

Cerebrovascular reactivity to carbon dioxide tension in newborns: Data from combined time-resolved near-infrared spectroscopy and diffuse correlation spectroscopy

Significance: Critically ill newborns are at risk of brain damage from cerebrovascular disturbances. A cerebral hemodynamic monitoring system would have the potential role to guide targeted intervention. Aim: To obtain, in a population of newborn infants, simultaneous near-infrared spectroscopy (NIRS)-based estimates of cerebral tissue oxygen saturation (StO2) and blood flow during variations of carbon dioxide tension (pCO2) levels within physiologic values up to moderate permissive hypercapnia, and to examine if the derived estimate of metabolic rate of oxygen would stay constant, during the same variations. Approach: We enrolled clinically stable mechanically ventilated newborns at postnatal age >24 h without brain abnormalities at ultrasound. StO2 and blood flow index were measured using a non-invasive device (BabyLux), which combine time-resolved NIRS and diffuse-correlation spectroscopy. The effect of changes in transcutaneous pCO2 on StO2, cerebral blood flow (CBF), and cerebral metabolic rate of oxygen index (tCMRO2i) were estimated. Results: Ten babies were enrolled and three were excluded. Median GA at enrollment was 39 weeks and median weight 2720 g. StO2 increased 0.58% (95% CI 0.55; 0.61, p < 0.001), CBF 2% (1.9; 2.3, p < 0.001), and tCMRO2 0.3% (0.05; 0.46, p 0.017) per mmHg increase in pCO2. Conclusions: BabyLux device detected pCO2-induced changes in cerebral StO2 and CBF, as expected. The small statistically significant positive relationship between pCO2 and tCMRO2i variation is not considered clinically relevant and we are inclined to consider it as an artifact

Effects of red blood cell transfusion on neonatal cerebral hemodynamics: a TD-NIRS and DCS study

Anemia is a common problem in preterm neonates, and red blood cell transfusion (RBCT) is used to improve oxygen delivery. In order to limit the risk of possible complications new strategies to minimize the need for RBCTs are needed, as assessment of hemoglobin concentration in blood ([Hb]) alone appears to be an inadequate biomarker. In this study, we search for hemodynamic and metabolic thresholds to help define the need of RBCT in anemic newborns. The effect of RBCTs on cerebral tissue oxygen saturation (StO2) and blood flow (measured as Blood Flow Index, BFI) was estimated using a non-invasive hybrid diffuse optical device that combines Time Domain NIRS (TD-NIRS) and Diffuse Correlation Spectroscopy (DCS) techniques (BabyLux device). We enrolled 18 clinically stable neonates receiving RBCT at Neonatal Intensive Care Unit (NICU) of Ospedale Maggiore Policlinico in Milan. Tissue oxygen extraction (TOE) and the cerebral metabolic rate of oxygen consumption index (CMRO2I) were computed, the Wilkinson signed rank test for paired data was performed to compare data before and after RBCT. Preliminary results are in accordance with previous publications as regards cerebral oxygenation: a significant increase in StO2 (from 56.62 ± 5.20% to 63.85 ± 4.95%, p<0.05) and reduction in TOE (from 41.35 ± 5.9 % to 31.04 ±5.41%, p<0.05) were observed. The response in cerebral blood flow was smaller (only 10%) but also more variable, so conclusions regarding the effect of transfusion on cerebral oxygen metabolism are still uncertain

Both selective and neutral processes drive GC content evolution in the human genome

Mammalian genomes consist of regions differing in GC content, referred to as isochores or GC-content domains. The scientific debate is still open as to whether such compositional heterogeneity is a selected or neutral trait. RESULTS: Here we analyze SNP allele frequencies, retrotransposon insertion polymorphisms (RIPs), as well as fixed substitutions accumulated in the human lineage since its divergence from chimpanzee to indicate that biased gene conversion (BGC) has been playing a role in within-genome GC content variation. Yet, a distinct contribution to GC content evolution is accounted for by a selective process. Accordingly, we searched for independent evidences that GC content distribution does not conform to neutral expectations. Indeed, after correcting for possible biases, we show that intron GC content and size display isochore-specific correlations. CONCLUSION: We consider that the more parsimonious explanation for our results is that GC content is subjected to the action of both weak selection and BGC in the human genome with features such as nucleosome positioning or chromatin conformation possibly representing the final target of selective processes. This view might reconcile previous contrasting findings and add some theoretical background to recent evidences suggesting that GC content domains display different behaviors with respect to highly regulated biological processes such as developmentally-stage related gene expression and programmed replication timing during neural stem cell differentiation

Maternal sensitivity buffers the association between SLC6A4 methylation and socio-emotional stress response in 3-month-old full term, but not very preterm infants

Background: Very preterm (VPT) infants are hospitalized in Neonatal Intensive Care Units (NICUs) and are exposed to life-saving procedures eliciting pain-related stress. Recent research documented that pain-related stress might result in birth-to-discharge increased methylation of serotonin transporter gene (SLC6A4) in VPT infants, leading to poorer stress regulation at 3 months of age in VPT infants compared to their full-term (FT) counterparts. Maternal sensitivity is thought to support infants' stress response, but its role in moderating the effects of altered SLC6A4 methylation is unknown. Main aim: To assess the role of maternal sensitivity in moderating the association between altered SLC6A4 methylation and stress response in 3-month-old VPT and FT infants. Methods: 53 infants (27 VPTs, 26 FTs) and their mothers were enrolled. SLC6A4 methylation was obtained from peripheral blood samples at NICU discharge for VPT infants and from cord blood at birth for FT infants. At 3 months (age corrected for prematurity), both groups participated to the face-to-face still-face (FFSF) paradigm to measure both infants' stress response (i.e., negative emotionality) and maternal sensitivity. Results: Maternal sensitivity did not significantly differ between VPT and FT infants' mothers. In VPT infants, higher SLC6A4 methylation at hospital discharge associates with higher negative emotionality during the FFSF. In FT infants, SLC6A4 methylation and maternal sensitivity significantly interacted to predict stress response: a positive significant association between SLC6A4 methylation and negative emotionality emerged only in FT infants of less-sensitive mothers. Discussion: Although no differences emerged in caregiving behavior in the two groups of mothers, maternal sensitivity was effective in moderating the effects of SLC6A4 methylation in FT infants, but not in VPT infants at 3 months. Speculatively, the buffering effect of maternal sensitivity observed in FT infants was disrupted by the altered early mother-infant contact due to NICU stay of the VPT group. These findings indirectly support that the effects of maternal sensitivity on infants' socio-emotional development might be time dependent, and that mother-infant interventions in the NICU need to be provided precociously within a narrow sensitive period after VPT birth

Oligometastatic Gastric Cancer: Clinical Data from the Meta-Gastro Prospective Register of the Italian Research Group on Gastric Cancer

Background: Interest in the field of metastatic gastric cancer has grown in recent years, and the identification of oligometastatic patients plays a critical role as it consents to their inclusion in multimodal treatment strategies, which include systemic therapy but also surgery with curative intent. To collect sound clinical data on this subject, The Italian Research Group on Gastric Cancer developed a prospective multicentric observational register of metastatic gastric cancer patients called META-GASTRO. Methods: Data on 383 patients in Meta-Gastro were mined to help our understanding of oligometastatic, according to its double definition: quantitative/anatomical and dynamic. Results: the quantitative/anatomical definition applies to single-site metastases independently from the metastatic site (p < 0.001) to peritoneal metastases with PCI ≤ 12 (p = 0.009), to 1 or 2 hepatic metastases (p = 0.024) and nodal metastases in station 16 (p = 0.002). The dynamic definition applies to a percentage of cases variable according to the metastatic site: 8%, 13.5 and 23.8% for hepatic, lymphatic and peritoneal sites, respectively. In all cases, the OS of patients benefitting from conversion therapy was similar to those of cases deemed operable at diagnosis and operated after neoadjuvant chemotherapy. Conclusions: META-GASTRO supports the two-fold definition of oligometastatic gastric cancer: the quantitative/anatomical one, which accounts for 30% of our population, and the dynamic one, observed in 16% of our cases

NUTRITIONAL AND DIGESTIVE EFFECTS OF GASTRECTOMY FOR GASTRIC CANCER

Background: Gastrectomy often leads to malnutrition. Objective: The aim of this study was to analyze nutritional and digestive effects of gastrectomy for cancer. Patients and methods: Gastrectomized patients were studied by nutritional assessment including a weekly nutritional diary exploring digestive symptoms. Results: Thirty-two patients were analyzed after a mean follow-up of 41.8 months. The mean percentage of weight loss was 12.9% \ub1 13.5%. After total gastrectomy, mean weight loss was 22% \ub1 1.2%, against 7.4% \ub111.9% for subtotal gastrectomy (p = 0.002). Moreover, advancing age was related to weight loss (p = 0.02), with a peak around 70 years. The most frequent postprandial symptoms were abdominal swelling (62%) and early satiety (59%). Finally, findings of the present study imply that overm a long follow-up, there are no specific intolerances related to gastrectomy. Conclusions: Patients who have undergone a total gastrectomy and elderly gastrectomized patients are at risk of malnutrition and need postoperative nutritional support

Prognostic Value of a 6-Minute Walk Test in Patients With Transthyretin Cardiac Amyloidosis

Background The 6-minute walk test (6MWT) represents a comprehensive functional assessment that is commonly used in patients with heart failure; however, data are lacking in patients with transthyretin cardiac amyloidosis (ATTR-CA). Objectives This study aimed to assess the prognostic importance of the 6MWT in patients with ATTR-CA.Methods A retrospective analysis of patients diagnosed with ATTR-CA at the National Amyloidosis Centre who underwent a baseline 6MWT between 2011 and 2023 identified 2,141 patients, of whom 1,118 had follow-up at 1 year.Results The median baseline 6MWT distance was 347 m (Q1-Q3: 250-428 m) and analysis by quartiles demonstrated an increased death rate with each distance reduction (deaths per 100 person-years: 6.3 vs 9.2 vs 13.6 vs 19.0; log-rank P &lt; 0.001). A 6MWT distance of 35 m) and relative worsening (reduction of &gt;5%) of 6MWT at 1 year was associated with an increased risk of mortality (HR: 1.80; 95% CI: 1.51-2.15; P &lt; 0.001 and HR: 1.89; 95% CI: 1.59-2.24; P &lt; 0.001, respectively), which was similar across the aforementioned subgroups. When combined with established measures of disease progression (N-terminal pro–B-type natriuretic peptide progression and outpatient diuretic intensification), each incremental increase in progression markers was associated with an increased death rate (deaths per 100 person-years: 7.6 vs 13.9 vs 22.4 vs 32.9; log-rank P &lt; 0.001). Conclusions The baseline 6MWT distance can refine risk stratification beyond traditional prognosticators. A worsening 6MWT distance can stratify disease progression and, when combined with established markers, identifies patients at the highest risk of mortality